Protocols and Supplementary Data

Gilad Lab Wiki (permission required)

Protocols

LCL Reprogramming Protocol  written

This protocol outlines the procedure used in the lab to generate iPSCs from LCLs.

Epipedobates tricolor maintenance protocol written | visual

This protocol outlines maintenance procedures used in the lab for long term care of Epipedobates tricolor.

Publications with supplementary data

Single-cell sequencing reveals lineage-specific dynamic genetic regulation of gene expression during human cardiomyocyte differentiation

Elorbany R, Popp JM, Rhodes K, Strober BJ, Barr KA, Qi G, Gilad Y, and Battle A

PLoS Genetics; 2022

Supplementary data: upload pending

Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis

Hsiao CJ, Tung P, Blischak JD, Burnett J, Barr K, Dey KK, Stephens M, and Gilad Y

Genome Research; 2020

Supplementary data: TAR.GZ file

A comparative study of endoderm differentiation in humans and chimpanzees

Blake LE, Thomas SJ, Blischak JD, Hsiao C, Chavarria C, Myrthil M, Gilad Y, Pavlovic BJ

Genome Biology; 2018

Supplementary data: XLS file

Integrated Analyses of Gene Expression and Genetic Association Studies in a Founder Population

Cusanovich DA, Caliskan M, Billstrand C, Michelini K, Chavarria C, De Leon S, Mitrano A, Lewellyn N, Elias JA, Chupp GL, Lang RM, Shah SJ, DeCara JM, Gilad Y, and Ober C

Human Molecular Genetics; 2016

Supplementary data: ZIP file

 

Genetic Variation, Not Cell Type of Origin, Underlies the Majority of Identifiable Regulatory Differences in iPSCs

Burrows CK, Banovich NE, Pavlovic BJ, Patterson K, Gallego Romero I, Pritchard JK, and Gilad Y

PLoS Genetics; 2016

Supplementary data: ZIP file

Mycobacterial infection induces a specific human innate immune response

Blischak JD, Tailleux L, Mitrano A, Barreiro L, and Gilad Y

Scientific Reports; 2015

Supplementary data: ZIP file

A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics

Gallego Romero I, Pavlovic BJ, Hernando-Herraez I, Zhou X, Ward MC, Banovich NE, Kagan CL, Burnett JE, Huang CH, Mitrano A, Chavarria CI, Friedrich Ben-Nun I, Li Y, Sabatini K, Leonardo TR, Parast M, Marques-Bonet T, Laurent LC, Loring JF, Gilad Y

eLife; 2015

Supplementary data: TXT file

Impact of regulatory variation from RNA to protein

Battle A, Kahn Z, Wang SH, Mitrano A, Ford MJ, Pritchard JK, and Gilad Y

Science; 2015

Supplementary data: ZIP file

Genotype data and RNA sequencing data from the 72 YRI LCL lines used in this study are available on GEO (GSE19480 ) and GEUVADIS (E-GEUV-3; ArrayExpress), as is the ribosome profiling data generated in this study (GSE61742). The YRI LCLs have also been used to measure a variety of genomic phenotypes, including H3K27ac (GSE58852), DNA methylation (GSE57483), chromatin accessibility (DNAse-seq; GSE31388), transcriptional elongation rates and initiation frequencies (4sU-seq; GSE75220), RNA decay (GSE37451), and protein levels (PXD001406).

Methylation QTLs Are Associated with Coordinated Changes in Transcription Factor Binding, Histone Modifications, and Gene Expression Levels

Banovich NE, Lan X, McVicker G, van de Geijn B, Degner JF, Blischak JD, Roux J, Pritchard JK, and Gilad Y

PLoS Genetics; 2014

Supplementary data: TXT file

Social environment is associated with gene regulatory variation in the rhesus macaque immune system

Tung J, Barreiro LB, Johnson ZP, Hansen KD, Michopoulos V, Toufexis D, Michelini K, Wilson ME, and Gilad Y

Proceedings of the National Academy of Sciences; 2012

Supplementary data: TXT file

Comparative RNA sequencing reveals substantial genetic variation in endangered primates

Perry GH, Melsted P, Marioni JC, Wang Y, Bainer R, Pickrell JK, Michelini K, Zehr S, Yoder AD, Stephens M, Pritchard JK, and Gilad Y

Genome Research; 2012

Supplemental data: TGZ data

A genome sequence resource for the aye-aye (Daubentonia madagascariensis), a nocturnal lemur from Madagascar

Perry GH, Reeves D, Melsted P, Ratan A, Miller W, Michelini K, Louis EE Jr, Pritchard JK, Mason CE, and Gilad Y

Genome Biology and Evolution; 2012

Supplemental data: ZIP file

 

The effects of EBV transformation on gene expression levels and methylation profiles

Çalışkan M, Cusanovich DA, Ober C, and Gilad Y

Human Molecular Genetics; 2011

Supplemental data: ZIP file

Genomic-scale capture and sequencing of endogenous DNA from feces

Perry GH, Marioni JC, Melsted P, and Gilad Y

Molecular Ecology; 2010

Supplemental data and code: TAR.GZ file

Expression quantitative trait loci detected in cell-lines are often present in primary tissues

Bullaughey K, Chavarria CI, Coop G, and Gilad Y

Human Molecular Genetics; 2009

Supplementary data: ZIP file

Segmental duplications contribute to gene expression differences between humans and chimpanzees

Blekhman R, Oshlack A, and Gilad Y

Genetics; 2009

Supplementary data: ZIP file

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

Marioni JC, Mason CE, Shrikant MM, Stephens M, and Gilad Y

Genome Research; 2008

Supplementary data: ZIP file

Using reporter gene assays to identify cis regulatory differences between humans and chimpanzees

Chabot AE, Shrit RA, Blekhman R and Gilad Y

Genetics; 2007

Supplementary data: ZIP file

Using DNA microarrays to study gene expression in closely related species

Oshlack A, Chabot AE, Smyth GK and Gilad Y

Bioinformatics; 2007

Supplementary data: DOC file